The "I'm too lazy to click a link" version: it's frankly misogynistic to identify a competent female protagonist as a "Mary Sue" because she's at the center of her story. She's at the center of her story because she's the goddamn protagonist.
Why is The Lord of the Rings about Frodo? Because he's the hobbit with the ring. If a different hobbit had had the ring, the book/trilogy would have been about a different hobbit.
When I pick up a book called The Great Gatsby or Anna Karenina or The World According to Garp, I'm pretty sure that Gatsby/Anna/Garp are going to be central to the narrative. This works for books with titles like The Wind-up Girl and Who Fears Death (a name, if you have not read it) and The Lies of Locke Lamora too. Hey, there's a name or an epithet in the title. Maybe this book is about this person!
So... if you find yourself uncomfortable with a lot of books by female authors, with female protagonists, and identifying a high percentage of those female as "Mary Sues," well... it is possible that the fault lies not in the protagonists, but in the reader*.
Sometimes a book is about a female character because there are female people in the world.
Crazy talk, I know, but there you go.
*This also applies if you find yourself often dismissing books with queer central characters as "slash."** Sometimes books are about gay people because gay people exist.
**If you are a slash fan, and trying to sell a book to your friends, letting them know it has the manlove is different. I'm talking about the "Straight boys need not read this because it has The Ghey in it" reviews. They say more about the reviewer than the book, is all I'm saying.